GapMind for catabolism of small carbon sources

 

Protein HSERO_RS05195 in Herbaspirillum seropedicae SmR1

Annotation: HSERO_RS05195 xylose ABC transporter ATP-binding protein

Length: 518 amino acids

Source: HerbieS in FitnessBrowser

Candidate for 13 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-arabinose catabolism gguA hi GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized) 69% 99% 696.4 ATP binding protein of ABC transporter for pentoses, component of ABC sugar transporter that plays a role in the probiotic benefits through acetate production 55% 557.0
D-cellobiose catabolism mglA hi GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized) 69% 99% 696.4 ATP binding protein of ABC transporter for pentoses, component of ABC sugar transporter that plays a role in the probiotic benefits through acetate production 55% 557.0
D-galactose catabolism gguA hi GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized) 69% 99% 696.4 ATP binding protein of ABC transporter for pentoses, component of ABC sugar transporter that plays a role in the probiotic benefits through acetate production 55% 557.0
D-glucose catabolism mglA hi GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized) 69% 99% 696.4 ATP binding protein of ABC transporter for pentoses, component of ABC sugar transporter that plays a role in the probiotic benefits through acetate production 55% 557.0
lactose catabolism mglA hi GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized) 69% 99% 696.4 ATP binding protein of ABC transporter for pentoses, component of ABC sugar transporter that plays a role in the probiotic benefits through acetate production 55% 557.0
D-maltose catabolism mglA hi GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized) 69% 99% 696.4 ATP binding protein of ABC transporter for pentoses, component of ABC sugar transporter that plays a role in the probiotic benefits through acetate production 55% 557.0
sucrose catabolism mglA hi GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized) 69% 99% 696.4 ATP binding protein of ABC transporter for pentoses, component of ABC sugar transporter that plays a role in the probiotic benefits through acetate production 55% 557.0
trehalose catabolism mglA hi GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized) 69% 99% 696.4 ATP binding protein of ABC transporter for pentoses, component of ABC sugar transporter that plays a role in the probiotic benefits through acetate production 55% 557.0
D-xylose catabolism xylG hi GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized) 69% 99% 696.4 ATP binding protein of ABC transporter for pentoses, component of ABC sugar transporter that plays a role in the probiotic benefits through acetate production 55% 557.0
D-galactose catabolism mglA med Galactose/methyl galactoside import ATP-binding protein MglA; EC 7.5.2.11 (characterized) 44% 96% 398.3 GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter 69% 696.4
L-rhamnose catabolism rhaT' med RhaT, component of Rhamnose porter (Richardson et al., 2004) (Transport activity is dependent on rhamnokinase (RhaK; AAQ92412) activity (Richardson and Oresnik, 2007) This could be an example of group translocation!) (characterized) 41% 96% 377.5 GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter 69% 696.4
D-fructose catabolism frcA med ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale) 43% 92% 355.5 GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter 69% 696.4
sucrose catabolism frcA med ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale) 43% 92% 355.5 GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter 69% 696.4

Sequence Analysis Tools

View HSERO_RS05195 at FitnessBrowser

PaperBLAST (search for papers about homologs of this protein)

Search CDD (the Conserved Domains Database, which includes COG and superfam)

Predict protein localization: PSORTb (Gram negative bacteria)

Predict transmembrane helices and signal peptides: Phobius

Check the SEED with FIGfam search

Fitness BLAST: loading...

Sequence

MSNILEMRGIEKSFPGVKALNNVNLAVREGEIHAIVGENGAGKSTLMKVLSGVYPHGSYS
GDIVYKGEVRAFKDIRDSEHLGIIIIHQELALVPLLSVMENLFLGNEQARGGVIDWEQSY
VRAKELLAKVGLKESPLTQVGDLGVGKQQLIEIAKALSKEVKLLILDEPTASLNESDSDA
LLELLLELKRQGIASILISHKLNEISKVADSITVLRDGTTVDTFDCRAEPISEDRIIQHM
VGREMADRYPQRDPQIGEVIFEVRDWRVHHPLHTDRLAIKDVNMSVRAGEIVGIAGLMGA
GRTELAKSIFGRAYGKKITGQAFLHGKEVDLSTIEKAIAKGIAYVTEDRKGDGLVLEEDI
KKNISLANLGGVSERTVIDEAREYKIAADFKQQMRIRCSSVLQKVVNLSGGNQQKVVLSK
WLFSQPEVLILDEPTRGIDVGAKFEIYNIISKLAAEGKCIIMISSEMPELLGMCDRIYVM
NEGQFVGHLPKAEATQENIMRAIMRNKRIDEPGLSKAA

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory